Bioshock: Phoenix Rising
by Kyrte
Summary: AU. What if Sophia was able to succeed with Eleanor's moral conditioning? What if Delta was unable to save her? Follow the path of Alessa, a Big Sister with free will as she fights to find her Big Daddy, Subject Epsilon, save the Little Sisters and stop the Rapture Family. Some minor Eleanor bashing in this so be warned if you like her. Rated T for violence in later chapters.
1. Prologue

Disclaimer: I own nothing to do with Bioshock and this work is done for no profit. I am making no money from this and am just borrowing the characters out of love.

For ten long years he could feel nothing. And it hurt.

He knew who he was, but what he was, was a thing of the past. The humans he had fought to hard to protect were gone and these Demons had captured him. He knew it was over for him; his life would be taken from him.

_He heard the scream. One of the Scientists dragged in a child. The little girl was bleeding profusely and he struggled with the bonds they had placed him in as she cried for her Mother. _

"_Let her go!" He demanded and one of those who had dragged her in threw her down on the floor before spitting at the bound man. He cackled and grabbed the child again, shaking her in front of the furious man. _

"_Look, this is a real fighter kid! Pathetic, ain't he!" He cackled in glee at the thought. The little girl meanwhile looked at him and smiled, reaching out towards him with her free hand. _

"_You're shining." She said in awe and he stared at her as they strapped her down to the table. He screamed as they operated on her, feeling desperation claw at his mind. If he could just save her, if he could just save one child then he wouldn't have failed. He would have something to show for entering this hell._

_It was all for nothing. After what seemed like an age the child lay motionless on the table, blood dripping from the gaping hole in her stomach. Everyone waited as she stirred, and impossibly sat up. Glowing yellow eyes smiled at the stunned Angel and she jumped down from the table to beam up at him. _

"…_Good girl." One of the female Doctors took her hand and led her away, knowing that behind them her counterparts were already strapping the man to the same table, preparing him for the transformation into the new gatherer's protector. _

The next time he had seen the child, she had clambered up to him, smiling in joy at finally meeting her "Daddy." Though part of him knew it was impossible the rush of emotion he felt at the child's appearance overwhelmed him. Memories of the past faded away; all that mattered was the girl.

Their love was born in a lab, baptised with chemicals. Neither had intended it; he had his own duties and surely she had never intended to be taken from her parents. Yet beyond what was created their relationship had grown. He had indulged her childish games, carried her on his back through the trees, teaching her the safe fruits to eat and letting her pick them herself. She would drop from the branches, giggling as he caught her and set her on the ground.

"_I'm always safe with Daddy."_

Trapped deep within the confines of his cell he wept as he silently called out for his little girl. She needed him here, with him. Only then would they be whole.


	2. Awakening

**Disclaimer: I do not own anything to do with Bioshock. All characters you recognise belong to their respective owners and I make no money from this.**

* * *

She woke into pain, screaming as the electricity shocking her sent her muscles into spasms. With sheer effort of will she forced them to stop and stared wildly ahead, seeing the coldness of her cell around her.

"_Ah, __I see you are awake. That is good. Now, break your restraints."_ The voice came from the radio above her and like an obedient dog she flexed her arms, pulling at the chains. Almost too easily they snapped and she fell to her knees.

"_Vonderbar, little one. __You have been sleeping for a very long time. Now, my name, it is Tenebaum. Please, come and find me in the Atlantic Express Train Station." _

She staggered out of the cell into a brightly lit corridor and found a small girl waiting for her. The child looked innocently up at the older female and smiled, holding up a small present.

"Mama says that you needed a present." She said softly and the female opened it to find several first aid kits, a crossbow with several bolts, a large needle like bracer and a small hypo. The girl smiled at her and spun around on one leg. "It's so good that you're awake. Mama Tenebaum says you're going to be a good Big Sister and keep us safe!"

The female didn't reply. Instead she slotted the Bracer onto her right arm, placed the crossbow on her back and packed the first aid kits, bolts and hypo into packs on her waist. Looking behind the girl she saw a small torn basket and hefted it onto her back without a second thought. Kneeling the girl scrambled up her back and settled into the basket with a small smile.

"Let's go Big Sister!" She cheered and at a run, the female raced through the halls, jumping across large gaps and at one point even venturing outside into the dark ocean. The heavy helmet she wore along with the suit meant she felt nothing more than a faint pressure. She froze though when she heard a terrifying scream in front of her. The little girl squeezed her shoulder and shrank down into the basket.

"Big Sister! Mean peoples!" She yelled and the female felt something take over her. The being within her screamed and an inhuman screech emerged from her throat. Holding out the bracer the needle shot out and she unhooked the crossbow from her back. Leaping into the air she saw the beings below her surrounding another child and in mid air, shot two of them through the head. Landing in front of the child she stabbed one with the needle and winced when a shot hit her shoulder. The girl shrank down in the basket and yelled at the being who shot her Big Sister.

"Big Sister's gonna give you stars and ouchies!" She yelled and under her helmet the Big Sister smiled grimly. Using a strength she didn't know she possessed the female held out her hand and with unseen force dragged him onto her needle. Draining the glowing blood from him she quickly unfastened the front of her helmet to gulp down the blood. Snapping it shut again she knelt down as the little girl in the basket held out her hand to the small child who was shaking from her fear.

"It's okay, Big Sister won't let anything happen to us!" She said happily and the small girl turned her own glowing yellow eyes onto the helmeted figure. "Big Sister?" She asked and the female screeched softly, nodding her head. Smiling then she scrambled up her back and squeezed into the basket alongside the other girl. Suddenly the female screeched and fell to her knees as a tremendous pressure squeezed her head. In the midst of the pain she could see dark blue eyes and stared in shock as they seemed to pierce her very soul.

"_**So. The good Doctor has woken up something that should have remained dead. I know you, Sister. I know that you will come for **__**him. To save yourself you would doom us all."**_

The female screeched and held her head as the voice echoed within it.

"_**Know th**__**is, Sister. The Doctor is not your friend, nor your ally. Within this city there is only one truth, the power and glory of the family."**_

The speakers around the small group crackled once more as the familiar voice rang out.

"_And now you see the enemy we b__oth share. That is Eleanor Lamb, daughter of Sophia Lamb, creator of the Family__.__ Now Sophia rules Rapture with Eleanor as her adoring pupil. She was once like you, what the little ones call a Big Sister. You are a very old Big Sister child__,__ one of the first this hell created, bonded for life as a child to a single protector, your Big Daddy. Rapture's Rulers changed you both, turning you into the Frankensteins you are now, but you still have your minds." _

The female cocked her head to one side and started walking towards the place she knew she had to be. Her charges were chattering away to each other when she finally came to the station. Absently shooting a female monster in the chest as she walked in she looked around the room. "Big Sister! Over there!" One of the little girls pointed to a button and the female pressed it. Behind the glass a screen rose and she saw several of the small children playing in a small room. A middle aged woman walked up to the screen and pressed a button, making the speakers crackle.

"_Big Sister, you are here as the little ones said you would be. Now you see why I am__ here. These little ones have been stolen from their parents like you were, long ago. This is my penance, to save them from your fate. Now, Eleanor and Sophia Lamb will stop at nothing to destroy us, we who work to save the little ones-"_

At those words the female fell to her knees, a pained screech tearing itself from her lips as she felt the memories of the older female come to the forefront of her mind. Feeling warm hands help her up she staggered into the room and was placed on the bed there. Tenebaum gently unhooked the helmet on the female and placed it on the bed next to her as the two children clambered out of her basket.

"Breathe, little one. Eleanor is not here…" Tenebaum turned away for a moment, shaking her head as she looked at the children.

"Eleanor is no longer a protector to the little ones, no longer like you. She now rules this city alongside her Mother, and holds all the Big Daddies in prisons across the city. That includes your Father, Epsilon. She took control of all the Big Sisters, commanding them to kill any who stand in their mistress's way. That includes the little ones. You however, you are free from the conditioning. A lucky twist of fate led to you being held in cryogenic stasis, like your Father." The girl looked up and Tenebaum saw confusion in her glowing yellow eyes. Carefully the older woman stroked her head, brushing back the dark hair and the girl purred, curling into the embrace.

"Alone, you will not survive long in Rapture. You must find your Big Daddy and reinforce the pair bond between you. Together, you may stand a chance of escape from here…but I must ask one favour of you both. Please, try to save the little ones. Take them with you, away from this nightmare. Your Father will show you how, I am sure. Now, you shall need a name for when I contact you. In the records I have been able to find it appears your birth name was Alessa. I think that shall be quite suitable for you."

The female spent a week in that room, learning from Tenebaum. She found out that she was the last of the Big Sisters who still had their free will. However, she was hopelessly out of date compared to the others and Tenebaum spent many hours operating on her, removing the conditioning of Eleanor, the compulsion to serve her as well as upgrading her weapons and plasmid skills. Finally, she was ready. As she prepared to leave the room and head out Tenebaum handed her a ticket and smiled, one hand brushing against the cold metal helmet.

"I have an ally who will help guide you through this city waiting at the train station. Sinclair is a strange man, but he knows this place like the back of his hand. I am sure he will be able to get you to Epsilon very quickly. Any little ones you save I will protect here. Good luck Frau Alessa."

Alessa screeched softly at her, curling into the embrace before she ran out the door and into the darkness of Rapture. Tenebaum watched her go sadly as the little ones played around her. None of them seemed aware of the hell around them, none except the older woman who brushed away a tear. Silently she locked the door again, having done her part. The rest was up to Alessa and Sinclair.


	3. Meeting Sinclair

Disclaimer: I own nothing to do with the Bioshock franchise. I am only borrowing the concepts and characters for entertainment purposes and make no money from this.

* * *

"_Daddy, do you love me?__"_

_That single question, spoken with all the innocence of a child made her companion stop, one colossal hand raised to his shielded face as he mock-thought on it. The child laughed and scampered up to him, her hands held behind her back as she beamed up at the man who was her whole world. The man sat down heavily on the ground with an earth shattering sound and held out one hand to the child who clambered onto his leg. She held out her hands to him and hugged his arm, the only part she could reach around properly. His other arm held her close and he groaned softly to her in reply. She laughed and sat back to play with her small doll as he looked around, keeping a look out for the slightest danger._

_Finally she yawned and he picked her up, ready to deposit her back into the nearby vent. Though they hadn't collected much ADAM today he was feeling indulgent towards her. As he lifted her up towards the vent she scrambled inside before turning around and reaching out towards him._

"_Night Night Daddy, love you lots.__"__ She yawned before crawling away through the vent. Her Father groaned a farewell before turning around and slowly making his way through the trees, his only thought to find a safe place to stay until his Sister was ready to gather again._

* * *

Within the cold streets of Rapture the lights flickered softly over two figures crouched by a corpse. Dressed in ragged clothes heavy lesions were oozing pus from their bodies, their faces terribly disfigured as they ignored their many wounds. One was stabbing the corpse wildly while the other rifled through its pockets, searching for anything of use. Finally they stopped as one held up a small vial of green liquid triumphantly.

"I got it!" He said and howled as his companion smirked. Her hand was pressed against his stomach, where one of her hooks skewered his flesh. She smirked and twisted it sharply as he gasped.

"Looks like I'm the one who's got it, sweetie!" She hissed and pulled her hook free, sending his guts splattering across the floor. As he crumpled to the ground she caught the vial and held it delicately in her deformed hands. "All this sweet tasty ADAM…all for meee…" She sang softly when a loud screech made her jump. Picking the hooks up she scrambled towards the distant ceiling when she heard the screech again. The lights seemed to dim as she leapt frantically for the hole in the ceiling, only for something to pick her out of the air and slam her back into the ground.

The splicer staggered to her feet just in time for a long thin needle to stab her in the chest. Staring up in the half-light she felt tears come to her eyes as she looked into the crimson porthole of Rapture's Alpha predator. The Big Sister held her up and with the other hand, delicately removed the vial from the splicer. The female weakly protested and the Big Sister threw her down with a dismissive smash, chirping slightly as the splicer crawled feebly away. Shrugging her shoulders she unsnapped the front of her helmet and in a quick gulp downed the ADAM.

"_There you are!"_

Instantly the Big Sister shrieked and threw the vial against the wall. The voice chuckled as she searched for its owner. _"Right here kiddo. Would you go grab that radio for me? The one to your left."_ She trilled a soft confused sound but did as the voice said, seeing the small device sitting on the ground by the flickering street lights. Picking it up she tilted her head to one side, trilling softly to herself as she examined it. It buzzed and she dropped it with a shriek, making the owner of the broadcaster chuckle softly to himself. _"…It's okay Kiddo. I'm not gonna hurt you. Names Augustus Sinclair, Esquire. Tenebaum's told me to keep you supplied out in the field and let you i__n on what you'll need to know down here. Now, first rule of Rapture is only the strongest survive. If you'll pick the radio up and go sit by that window to your left you'll see what I mean."_

Alessa chirped softly to herself, but did as the voice asked and picked up the radio. Walking over to the other side of the street she paused at the edge of a viewing platform and looked behind her at the street. Suddenly an ear-splitting roar reverberated through the deserted place. Before Alessa could react several of the mutilated beings she had seen poured into the road, weapons firing from where they came. She growled softly and raised her syringe when the radio crackled again. _"Easy there Kiddo. Just stay outta the way. They've got bigger problems to worry about."_ It said and right on cue the wall gave way.

The beings screamed as what could only be described as a giant distorted version of the Big Sister raced through. It roared and raised its right hand, showing a large drill mounted in place of the flesh. The other hand sizzled with flames, quickly incinerating a hapless male who howled in agony. Alessa tilted her head to one side, chirping softly as she watched it advance upon its enemies. One creature shrieked and leapt into the air, throwing hooks at the creature; they embedded into his chest and he roared, the flames in his hand shooting up to incinerate her. One of the beings heard her screams and gasped as her skeleton dropped in front of him. Taking one last look at the Sister's doppleganger he fled, running into the shadows and leaving only two behind.

Alessa slumped to the floor, her head tilted to one side as she watched curiously. The giant picked up one of the mutilated beings and held him out at arms length for a long moment. The male choked, gasping for breath as he scrabbled at the cold metal arm holding him. Slowly, inexorably, the other arm raised itself up and the male could only stare into the twisted reflection the bronzed drill showed him.

"No!" He screamed.

The drill swung down, spinning as it bit deep into his chest. Blood spurted out and splattered the ruined floor, staining the already dusty concrete a bitter red. The sole survivor stared at the dying form of his comrade in horror. His gun fell from his hands and he shook as the large crimson porthole of this unstoppable being turned towards him. "…Please…" He breathed, shaking his head as he stumbled back. The armoured being seemed to regard him for a moment before the drill was raised again. With a mighty swing the survivor skidded along the floor, slamming into the debris gathering at the edges of the street. Blood trickled down the side of his head as it lolled forward lifelessly.

Alessa looked at the last one standing then looked down at the radio. Standing up she frowned as the being walked towards the centre of the street and the lights that flickered above him. She saw an amber porthole staring vacantly across the ground and froze.

"_Daddy, do you love me?__"_

Across the hall the Big Daddy jumped at the high pitched shriek emitted from behind him. He glanced around just in time to be assaulted by a small metallic torpedo. At least, that's what it felt like. The stunned Daddy looked down at the Big Sister who was latched onto his arm, nuzzling the worn armoured fabric affectionately. She trilled a greeting to the Daddy who groaned, regarding her with nothing short of indifference. Pushing her off him he raised the drill in warning before lumbering away. Behind him Alessa sat up, her porthole glowing amber as she watched the Daddy walk away from her. Soft growls echoed from within the helmet as a lifetime of conditioning was trodden on by one indifferent Daddy.

She threw her head back and an ear piercing shriek ripped itself from her throat. The Radio was buzzing but she was hardly aware of it until a jolt of electricity made her jump. Opening her eyes she saw a security bot hovering in front of her. _"Hey! You stop that right now Kiddo. That Big Daddy might look like your pops but he'll rip your arms of__f with half a chance.__"_ Alessa stood up at Sinclair's words and shook her head, her whole body slouched and dejected. Reluctantly she picked up the radio again and looked at it as it spoke.

"_Look, Kid. I know that what happened to you has messed you up good and proper but that Daddy ain't your real Daddy. That's just a poor soul who lost his own little Sister and you can't do anything for that guy now. It's best to forget about him Kid; focus instead on getting your own Daddy back. Now I've managed to procure us some transport so I want you to head to the Train Station in down town where we can pool our resources, so to speak. This bot will guide you there.__"_

The Radio dulled and Alessa chirped, shaking it slightly in her free hand. Nothing came out of it so she did the only thing that seemed logical. Placing it in the basket on her back she looked around the street she had stopped in, glanced quickly at the corpses around her and walked away, ignoring them completely. Whispers followed the sole Sister as she stalked through the streets after the whirring bot. She half-skipped, half ran across the ruined paths, on guard for any that thought a Big Sister alone would be an easy meal. Luckily none of the Splicers that watched her progress were degraded enough to try; only a few even daring to show themselves to her. Word had spread of the Big Sister's arrival and while they knew of the ADAM she carried they also knew the penalties the Family imposed upon any who managed to bring one of the Family's Agents down.

Alessa was largely unaware of the impact she had upon the Splicers within Rapture. While her conditioning was to keep a constant watch for danger her thoughts were on her Father. All she could comprehend was a dull ache in her chest that seemed to grow heavier when her Father was on her mind. Shaking her head slightly she paused as the bot stopped beside a large cast Iron door; Alessa looked around before tilting her head quizzically at the bot. _"__…You're here Kiddo, all you gotta do is open the door and we can finally meet. I'm pretty sure someone with your talents should be able to take out a little iron door.__"_She jumped at the Radio's voice and looked behind her, a loud screech registering her disapproval of Sinclair's voice. Turning back to the door she frowned, trying to figure out the answer to the puzzle of the door.

An age passed before she screeched in delight as the thought of the Big Daddy came back to her. Taking a small skip back away from the door Alessa looked up at it and raised her hands. Focusing on her gloved palms a soft red glow appeared. Underneath the helmet sweat dripped down Alessa's face, her body protesting the sudden influx of ADAM it was demanding. Ignoring the pain she roared and the glow burst into flames licking against her skin. Still she kept going, feeding the flames more ADAM as they grew steadily hotter. The instant the flames turned blue-white she threw them at the door, the metal melting away slowly as she applied more heat to it. Soft sounds escaped her helmet while Alessa worked, carefully melting away every last metal drop.

"Well Hey there Kiddo, nice of you to join the party." A familiar voice from within the room the door was protecting made Alessa wary. She raised the syringe and growled, the same strength within her letting her climb to the ceiling. Seeing a shadow moving about just outside the ticket office her porthole turned crimson and she leapt down with a screech.

"Hey!" Her target looked up at her cry and dodged to one side, holding a wrench up against her. He backed away slowly as Alessa got to her feet and held his hands up in surrender. "It's me Kid, it's Sinclair…I-I'm here to help you!" He finished almost shouting at the Sister. Alessa growled at him and took a step forward as he fumbled about with a small device in his hands. Rushing towards him Alessa jumped when the Radio in her basket whirred to life again, distracting her from her goal. _"__Look! It's me! Sinclair!"_ It said and she trilled angrily at it when she heard an echo of the words. Her porthole turned towards her target and she paused when she saw him speaking into the device in his hands. He turned it off and she looked curiously at him, unsure what to think.

From the other side of things Sinclair looked at the Sister. She had stopped mid-blow thanks to his quick thinking with the Radio; now she was just watching him through that damn helmet of hers. As he watched her he noticed the worn suit she wore; the dented helmet and meagre weapons supply and sighed, shaking his head at the poor state the sister was in despite Tenenbaum's insistence she had brought her up to full strength. "…Well you're in a worse state than the last guy I had the pleasure of escorting through Rapture…" He mused out loud when he suddenly noticed her porthole was no longer Red. A soft amber it gave him hope that somewhere deep within the torn fragments of her mind Alessa was starting to recognise him as a friend.

The Big Sister on the other hand felt once again, confusion. She didn't know what to think; from the moment she had awoken she had been directed, told what to do. This was the first time she had to make a choice. Trust or not to trust? It was difficult for her to even comprehend it but as she examined the male she noticed he wasn't fighting over ADAM, nor was he attacking her. All he did was watch and wait, his weapon held loosely at his side.

"_Daddy, the nasty people bashed another people today…it was scary."_

She flinched as a fragment of an image came to her mind. Within the child-like processes she remembered a man dying, killed by the Splicers. Her Daddy had taken her away from them, kept her safe. Alessa tried to hold onto the fragment, to remember what happened next but it slipped away from her. Yet it gave her one thing; what she needed right now.

Mean people hurt each other. He wasn't hurting her. So he couldn't be a mean person.

The porthole turned green and Sinclair breathed a sigh of relief. Rubbing the back of his head he jumped when he heard shouts in the distance and shook his head. "Well that's a relief. You know, for a second there I thought you were going to send me onto meet my maker early. Names Augustus Sinclair but you already know that." He said and Alessa merely watched him, finding the strange man amusing to look at. He motioned behind him, where a beaten and torn carriage awaited them.

"Time for us to go Kid. I've got us a first class transport for our little journey and while we head to our first destination I can fill you in on what little I've managed to find out on your Daddy's whereabouts." Alessa purred in delight at that, recognising the word Daddy and scampered up the stairs behind him to stand in the middle of the carriage. Sinclair chuckled at her and strolled in after her to start up the engine and get them on their way.

"I sure hope Tenenbaum's right about you Kid." He said to himself as Alessa looked at him, her helmet still glowing that reassuring green. Sighing softly as the carriage started to move he left the controls and went to open up a case lying abandoned on the floor. Pulling out a handful of weathered papers he sat down at a table and began to organise his research, one eye still on the Sister.

"…I don't think I've got it in me to lose another one."


End file.
